The current spraying of agrochemicals is unselective and ineffective, consuming a high amount of fungicides, which endangers the environment and human health. Cellulose-based nanocarriers (NCs) are a promising tool in sustainable agriculture and suitable vehicles for stimuli-responsive release of agrochemicals to target cellulase-segregating fungi, which cause severe plant diseases such as Apple Canker. Herein, cellulose was modified with undec-10-enoic acid to a hydrophobic and cross-linkable derivative, from which NCs were prepared via thiol-ene addition in miniemulsion. During the crosslinking reaction, the NCs were loaded in situ with hydrophobic fungicides, Captan and Pyraclostrobin. NCs with average sizes ranging from 200 to 300 nm and an agrochemical-load of 20 wt% were obtained. Cellulose-degrading fungi, e.g. Neonectria. ditissima which is responsible for Apple Canker, lead to the release of fungicides from the aqueous NC dispersions suppressing fungal growth. In contrast, the non-cellulase segregating fungi, e.g. Cylindrocladium buxicola, do not degrade the agrochemical-loaded NCs. This selective action against Apple Canker fungi, N. ditissima, proves the efficacy of NC-mediated drug delivery triggered by degradation in the exclusive presence of cellulolytic fungi. Cellulose NCs represent a sustainable alternative to the current unselective spraying of agrochemicals that treats many crop diseases ineffectively.